Sample Resequencing Stats

Note: The mutation counts shown below represent unfiltered mutation sets.

ALE, Flask, Isolate	Predicted Mutations	Mean Coverage	Total Reads	Percent Mapped	Mapped Reads	Average Read Length
A2 F1 I0 R1	4577	57.4	3436498	77.7%	2670158	63.4

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	minE	2,775,071	G→T	73.1%	L426L (CTG→CTT)	aceK →	isocitrate dehydrogenase kinase/phosphatase

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	minE	2,775,071	0	G	T	73.1%	62.3 / 27.6	52	L426L (CTG→CTT)	aceK	isocitrate dehydrogenase kinase/phosphatase
Reads supporting (aligned to +/- strand): ref base G (8/6); new base T (26/12); total (34/18)
Fisher's exact test for biased strand distribution p-value = 5.19e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

ATTCGCCATCTTTATATTGAGCGGCGGATGGTGCCGCTCAATATCTGGCTGGAACAAGTGGAAGGTCAGCAGTTGCGCGACGCCATTGAAGAATACGGTAACGCTATTCGCCAG  >  minE/2775021‑2775134

aTTCGCCATCTCTATATCGAACGACGGATGGTGCCGCTTAATATCTGGCTTGAGCAAGTTGAGGGGca                                                >  1:397259/1‑68 (MQ=255)

aTTCGCCATCTCTATATCGAACGACGGATGGTGCCGCTTAATATCTGGCTTGAGCAAGTTGAGGGGca                                                >  1:2381350/1‑68 (MQ=255)

aTTCGCCATCTCTATATCGAACGACGGATGGTGCCGCTTAATATCTGGCTTGAGCAAGTTGAGGGGca                                                >  1:2439212/1‑68 (MQ=255)

aTTCGCCATCTCTATATCGAACGACGGATGGTGCCGCTTAATATCTGGCTTGAGCAAGTTGAGGGGca                                                >  1:2691938/1‑68 (MQ=255)

aTTCGCCATCTCTATATCGAACGACGGATGGTGCCGCTTAATATCTGGCTTGAGCAAGTTGAGGGGca                                                >  1:2764314/1‑68 (MQ=255)

aTTCGCCATCTCTATATCGAACGACGGATGGTGCCGCTTAATATCTGGCTTGAGCAAGTTGAGGGGca                                                >  1:2893464/1‑68 (MQ=255)

aTTCGCCATCTCTATATCGAACGACGGATGGTGCCGCTTAATATCTGGCTTGAGCAAGTTGAGGGGca                                                >  1:3016130/1‑68 (MQ=255)

aTTCGCCATCTCTATATCGAACGACGGATGGTGCCGCTTAATATCTGGCTTGAGCAAGTTGAGGGGca                                                >  1:3330624/1‑68 (MQ=255)

aTTCGCCATCTCTATATCGAACGACGGATGGTGCCGCTTAATATCTGGCTTGAGCAAGTTGAGGGGca                                                >  1:343182/1‑68 (MQ=255)

aTTCGCCATCTCTATATCGAACGACGGATGGTGCCGCTTAATATCTGGCTTGAGCAAGTTGAGGGGca                                                >  1:2895793/1‑68 (MQ=255)

aTTCGCCATCTCTATATCGAACGACGGATGGTGCCGCTTAATATCTGGCTTGAGCAAGTTGAGGGGca                                                >  1:416654/1‑68 (MQ=255)

aTTCGCCATCTCTATATCGAACGACGGATGGTGCCGCTTAATATCTGGCTTGAGCAAGTTGAGGGGca                                                >  1:427327/1‑68 (MQ=255)

aTTCGCCATCTCTATATCGAACGACGGATGGTGCCGCTTAATATCTGGCTTGAGCAAGTTGAGGGGca                                                >  1:554138/1‑68 (MQ=255)

aTTCGCCATCTCTATATCGAACGACGGATGGTGCCGCTTAATATCTGGCTTGAGCAAGTTGAGGGGca                                                >  1:636231/1‑68 (MQ=255)

aTTCGCCATCTCTATATCGAACGACGGATGGTGCCGCTTAATATCTGGCTTGAGCAAGTTGAGGGGca                                                >  1:663250/1‑68 (MQ=255)

aTTCGCCATCTCTATATCGAACGACGGATGGTGCCGCTTAATATCTGGCTTGAGCAAGTTGAGGGGca                                                >  1:718915/1‑68 (MQ=255)

aTTCGCCATCTCTATATCGAACGACGGATGGTGCCGCTTAATATCTGGCTTGAGCAAGTTGAGGGGca                                                >  1:937849/1‑68 (MQ=255)

aTTCGCCATCTCTATATCGAACGACGGATGGTGCCGCTTAATATCTGGCTTGAGCAAGTTGAGGGGca                                                >  1:2295810/1‑68 (MQ=255)

aTTCGCCATCTCTATATCGAACGACGGATGGTGCCGCTTAATATCTGGCTTGAGCAAGTTGAGGGGca                                                >  1:2283845/1‑68 (MQ=255)

aTTCGCCATCTCTATATCGAACGACGGATGGTGCCGCTTAATATCTGGCTTGAGCAAGTTGAGGGGca                                                >  1:126538/1‑68 (MQ=255)

aTTCGCCATCTCTATATCGAACGACGGATGGTGCCGCTTAATATCTGGCTTGAGCAAGTTGAGGGGca                                                >  1:2270577/1‑68 (MQ=255)

aTTCGCCATCTCTATATCGAACGACGGATGGTGCCGCTTAATATCTGGCTTGAGCAAGTTGAGGGGca                                                >  1:216585/1‑68 (MQ=255)

aTTCGCCATCTCTATATCGAACGACGGATGGTGCCGCTTAATATCTGGCTTGAGCAAGTTGAGGGGca                                                >  1:1844964/1‑68 (MQ=255)

aTTCGCCATCTCTATATCGAACGACGGATGGTGCCGCTTAATATCTGGCTTGAGCAAGTCGAGGGGca                                                >  1:1215625/1‑68 (MQ=255)

aTTCGCCATCTCTATATCGAACGACGGATGGTGCAGCTTAATATCTGGCTTGAGCAAGTTGAGGGGca                                                >  1:1013973/1‑68 (MQ=255)

aTTCGCAATCTCTATATCGAACGACGGATGGTGCCGCTTAATATCTGGCTTGAGCAAGTTGAGGGGca                                                >  1:7289/1‑68 (MQ=255)

 ttCGCCATCTTTATATTGAGCGGCGGATGGTGCCGCTCAATATCTGGCTGGAACAAGTGGAAGGTcagc                                              >  1:2214537/1‑69 (MQ=255)

 ttCGCCATCTTTATATTGAGCGGCGGATGGTGCCGCTCAATATCTGGCTGGAACAAGTGGAAGGTcagc                                              >  1:616181/1‑69 (MQ=255)

 ttCGCCATCTTTATATTGAGCGGCGGATGGTGCCGCTCAATATCTGGCTGGAACAAGTGGAAGGTcagc                                              >  1:506630/1‑69 (MQ=255)

  tCGCCATCTTTATATTGAGCGGCGGATGGTGCCGCTCAATATCTGGCTGGAACAAGTGGAAGGTcagc                                              <  1:420986/68‑1 (MQ=255)

          tttATATTGAGCGGCGGATGGTGCCGCTCAATATCTGGCTGGAACAAGTGGAAGGTCAGCAGTTGcgcg                                     >  1:1484759/1‑69 (MQ=255)

               atTGAGCGGCGGATGGTGCCGCTCAATATCTGGCTGGAACAAGTGGAAGGTCAGCAGTTGCGCGACGc                                 <  1:2291331/68‑1 (MQ=255)

               atTGAGCGGCGGATGGTGCCGCTCAATATCTGGCTGGAACAAGTGGAAGGTCAGCAGTTGCGCGACGc                                 <  1:2531840/68‑1 (MQ=255)

                    gcggcgGATGGTGCCGCTCAATATCTGGCTGGAACAAGTGGAAGGTCAGCAGTTGCGCGACGCCATTg                            <  1:1423419/68‑1 (MQ=255)

                     cgacggATGGTGCCGCTTAATATCTGGCTTGAGCAAGTTGAGGGGCAGCAATTGCGTGATGCCATTgaa                          <  1:481778/66‑1 (MQ=255)

                     cgacggATGGTGCCGCTTAATATCTGGCTTGAGCAAGTTGAGGGGCAGCAATTGCGTGATGCCATTgaa                          <  1:779145/66‑1 (MQ=255)

                     cgacggATGGTGCCGCTTAATATCTGGCTTGAGCAAGTTGAGGGGCAGCAATTGCGTGATGCCATTgaa                          <  1:2628405/66‑1 (MQ=255)

                     cgacggATGGTGCCGCTTAATATCTGGCTTGAGCAAGTTGAGGGGCAGCAATTGCGTGATGCCATTgaa                          <  1:2757306/66‑1 (MQ=255)

                     cgacggATGGTGCCGCTTAATATCTGGCTTGAGCAAGTTGAGGGGCAGCAATTGCGTGATGCCATTgaa                          <  1:285096/66‑1 (MQ=255)

                     cgacggATGGTGCCGCTTAATATCTGGCTTGAGCAAGTTGAGGGGCAGCAATTGCGTGATGCCATTgaa                          <  1:1503174/66‑1 (MQ=255)

                     cgacggATGGTGCCGCTTAATATCTGGCTTGAGCAAGTTGAGGGGCAGCAATTGCGTGATGCCATTgaa                          <  1:2118915/66‑1 (MQ=255)

                      gacggATGGTGCCGCTTAATATCTGGCTTGAGCAAGTTGAGGGGCAGCAATTGCGTGATGCCATTgaa                          <  1:430523/66‑1 (MQ=255)

                      gacggATGGTGCCGCTTAATATCTGGCTTGAGCAAGTTGAGGGGCAGCAATTGCGTGATGCCATTgaa                          <  1:2022960/66‑1 (MQ=255)

                      gacggATGGTGCCGCTTAATATCTGGCTTGAGCAAGTTGAGGGGCAGCAATTGCGTGATGCCATTgaa                          <  1:3373729/66‑1 (MQ=255)

                      gacggATGGTGCCGCTTAATATCTGGCTTGAGCAAGTTGAGGGGCAGCAATTGCGTGATGCCATTgaa                          <  1:314571/66‑1 (MQ=255)

                       acggATGGTGCCGCTTAATATCTGGCTTGAGCAAGTTGAGGGGCAGCAATTGCGTGATGCCATTgaa                          <  1:792709/66‑1 (MQ=255)

                              gTGCCGCTCAATATCTGGCTGGAACAAGTGGAAGGTCAGCAGTTGCGCGACGCCATTGAAGAATACGGt                 <  1:2058630/69‑1 (MQ=255)

                                      cAATATCTGGCTGGAACAAGTGGAAGGTCAGCAGTTGCGCGACGCCATTGAAGAATACGGTAACGCTAt         >  1:3055271/1‑69 (MQ=255)

                                      cAATATCTGGCTGGAACAAGTGGAAGGTCAGCAGTTGCGCGACGCCATTGAAGAATACGGTAACGCTAt         >  1:293067/1‑69 (MQ=255)

                                      cAATATCTGGCTGGAACAAGTGGAAGGTCAGCAGTTGCGCGACGCCATTGAAGAATACGGTAACGCTAt         >  1:3313665/1‑69 (MQ=255)

                                      cAATATCTGGCTGGAACAAGTGGAAGGTCAGCAGTTGCGCGACGCCATTGAAGAATACGGTAACGCTAt         >  1:2537396/1‑69 (MQ=255)

                                           tCTGGCTGGAACAAGTGGAAGGTCAGCAGTTGCGCGACGc                                 <  1:3153752/40‑1 (MQ=255)

                                            ctggctggAACAAGTGGAAGGTCAGCAGTTGCGCGACGc                                 <  1:507736/39‑1 (MQ=255)

                                             tggctggAACAAGTGGAAGGTCAGCAGTTGCGCGACGCCATTGAAGAATACGGt                 <  1:1632142/54‑1 (MQ=255)

                                             tggctggAACAAGTGGAAGGTCAGCAGTTGCGCGACGCCATTGAAGAATACGGTAACGCTATTCGCCAg  >  1:1960533/1‑69 (MQ=255)

                                             tggctggAACAAGTGGAAGGGCAGCAGTTGCGCGACGCCATTGAAGAATACGGt                 <  1:2982734/54‑1 (MQ=255)

ATTCGCCATCTTTATATTGAGCGGCGGATGGTGCCGCTCAATATCTGGCTGGAACAAGTGGAAGGTCAGCAGTTGCGCGACGCCATTGAAGAATACGGTAACGCTATTCGCCAG  >  minE/2775021‑2775134

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 21 ≤` `ATCG/ATCG` `< 32 ≤` `ATCG/ATCG` `< 36 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A